Excellent!
Let me know if there is anything I can do to help.
-greg
On Tuesday, November 26, 2013, Paolo Tosco wrote:
> Dear James,
>
> I will try to get it done during the weekend - I'll get back to you once
> it's ready.
>
> Best,
> Paolo
>
>
> On 11/26/2013 05:51 PM, James Davidson wrote:
>
> Dear All,
>
>
>
> I think this is probably one for Paolo – I was looking at fixing certain
> atoms during MMFF minimisation, but couldn’t find the option… Then I
> re-read the UGM slides, and found the one titled “Force-field wish list”,
> and “fixed atoms” were one of the listed items!
>
>
>
> My intended use-case is the following:
>
>
>
> 1. Load protein-ligand complex into PyMOL
>
> 2. Make some changes to the bound ligand (using the Builder
> functionality)
>
> 3. Select atoms that are allowed to move (manual selection, then
> use of PyMOL’s ‘flag’ command)
>
> 4. Pass the molecule over to RDKit (already incorporated in a
> plugin we use), to minimise and then pass back (either as a new object, or
> apply the new coordinates to the existing object in situ)
>
>
>
> Actually, this process is already well-used by some of our chemists here –
> as a way of doing some simple modelling / idea exploration – but is
> currently using a much ‘flakier’ MMFF implementation. So I would
> definitely like to move to RDKit for the minimisation – any idea when a
> ‘fixed atoms’ option is likely to be added?
>
>
>
> Kind regards
>
>
>
> James
>
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> --
> ==========================================================
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> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
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